This sounds like something you should talk
through with Stata tech-support, but they'd need
precise details on your set-up. Perhaps
you are asking for so much memory that Stata
is using virtual memory and so becoming inordinately
slow.

Can you create an extract with fewer variables? Or perhaps run the
analysis on a random subsample of the data? You might do preliminary
analysis on a random subsample and then run final models on the entire data
set.